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Structure of a type II thymidine kinase with bound dttp
Analyse Structure of a type II thymidine kinase with bound dttp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W4R
- Type
- protein
- Length
- 1,303 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P04183
- Ligands
- TTP, ZN
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 174 | 32% helix, 27% strand | P04183 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 167 | 30% helix, 29% strand | P04183 |
| C, D, E, G | Thymidine kinase (EC 2.7.1.21) | protein | 160 | 29% helix, 29% strand | P04183 |
| F | Thymidine kinase (EC 2.7.1.21) | protein | 161 | 29% helix, 28% strand | P04183 |
| H | Thymidine kinase (EC 2.7.1.21) | protein | 161 | 29% helix, 29% strand | P04183 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.81 | 0.82 | 98 | TTP |
| 2 | 989 | 0.81 | 0.82 | 115 | empty |
| 3 | 645 | 0.76 | 0.82 | 78 | empty |
| 4 | 487 | 0.75 | 0.83 | 53 | DTU |
| 5 | 247 | 0.67 | 0.83 | 37 | TTP |
Interfaces
12 interfaces between chains.
- B–C · 1180 Ų buried · 32 hydrogen bonds · protein-protein
- E–H · 1180 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 1078 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1065 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04183
- Elsewhere: RCSB PDB 1W4R · PDBe 1W4R · UniProt P04183
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